Fig. 4

Depletion of microglia prevents activation of astrocytes. Mice were fed the CSF1R inhibitor PLX3397 in chow for 10 days prior to creation of organotypic brain slice cultures. Transcriptomic analysis was performed using NanoString from tissue harvested at DIV6. A Volcano plot of differential gene expression in PLX3397-fed mice. Note the robust decreases observed across a number of genes. B Pearson correlation matrix indicates a high correlation (r = 0.92) in mice that received standard chow relative to the previous DIV6 transcriptome presented in Fig. 2. Transcriptome derived from mice that were fed PLX3397 exhibits much lower correlations to both control transcriptomes. C Expression of genes that specific for distinct cell types indicate a decrease in both microglial and oligodendrocyte gene expression. D Organotypic brain slice cultures derived from PLX3397-fed mice do not exhibit transcriptomic changes that indicate a microglial disease state, do not show evidence for activation of astrocytes, do not exhibit increases in complement or inflammasome, and do not exhibit widespread decreases in neurotransmitter receptor genes. Scales for each heat map shown underneath and indicate Z-scores derived from Log₂[Fold Change]. X represents genes that were not detectable